The 40 mile stretch between Jefferson and Rocheport has some of the best scenery. Quite a single day ride though from Jefferson. The trail surface was good when I last rode there in 2019. The section between Matson & Machens is also quite popular, but it would be too far east to access by bike from Jefferson.
Overall, the scenery is best in the sections that closely follow the Missouri. I found the stretch between Booneville, where the trail leaves the river, and Clinton to be the least scenic.
I hope to get back out there in the near future, but it's a 16 hour drive from where I am in PA.